visit

About

VisIT is an
interactive parallel visualization and graphical analysis tool for
viewing scientific data on Unix and PC platforms.

VisIT is an interactive tool, and requires a login session to use.

Versions and Availability

Softenv Keys for visit on oliver

Machine

Version

Softenv Key

None Available

N/A

N/A

▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash
and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if
they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR
will cause things like rsync to break)

~/.bashrc (interactive login only)

~/.profile

When a user logs out of an interactive session, the
file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is
set automatically using SoftEnv. See below for more
information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's
environment if his login shell is /bin/tcsh.

Softenv

SoftEnv is a utility that is supposed to help users manage complex
user environments with potentially conflicting application versions
and libraries.

System Default Path

When a user logs in, the system /etc/profile
or /etc/csh.cshrc (depending on login shell, and mirrored
from csm:/cfmroot/etc/profile)
calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to
set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the
variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of
available packages. The listing will look something like:

Managing SoftEnv

The file ~/.soft in the user's home directory is where
the different packages are managed. Add the +keyword into your .soft
file. For instance, ff one wants to add the Amber Molecular Dynamics
package into their environment, the end of the .soft file should look
like this:

+amber-8

@default

To update the environment after modifying this file, one simply
uses the resoft command:

% resoft

The command soft can be used to manipulate the environment
from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user
to pay attention to possible order dependencies. That is, best results
require the user to remove keywords in the reverse order in which they
were added. It is handy to test out individual keys, but can lead to
trouble if changing multiple keys. Changing the .soft file and
issuing the resoft is the recommended way of dealing with
multiple changes.

Usage

You will need to add one of the following set of keys to your
software environment, depending on whether or not you want the
serial or parallel version:

Keys For Serial Use:

+gcc-4.3.2
+visit-1.12.1-gcc-4.3.2

Keys For Parallel Use:

+gcc-4.3.2
+mvapich-1.1-gcc-4.3.2
+visit-1.12.1-gcc-4.3.2-mvapich-1.1

Since upgrades will happen, verify the keys available
using the command: softenv -k.

▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash
and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if
they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR
will cause things like rsync to break)

~/.bashrc (interactive login only)

~/.profile

When a user logs out of an interactive session, the
file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is
set automatically using SoftEnv. See below for more
information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's
environment if his login shell is /bin/tcsh.

Softenv

SoftEnv is a utility that is supposed to help users manage complex
user environments with potentially conflicting application versions
and libraries.

System Default Path

When a user logs in, the system /etc/profile
or /etc/csh.cshrc (depending on login shell, and mirrored
from csm:/cfmroot/etc/profile)
calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to
set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the
variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of
available packages. The listing will look something like:

Managing SoftEnv

The file ~/.soft in the user's home directory is where
the different packages are managed. Add the +keyword into your .soft
file. For instance, ff one wants to add the Amber Molecular Dynamics
package into their environment, the end of the .soft file should look
like this:

+amber-8

@default

To update the environment after modifying this file, one simply
uses the resoft command:

% resoft

The command soft can be used to manipulate the environment
from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user
to pay attention to possible order dependencies. That is, best results
require the user to remove keywords in the reverse order in which they
were added. It is handy to test out individual keys, but can lead to
trouble if changing multiple keys. Changing the .soft file and
issuing the resoft is the recommended way of dealing with
multiple changes.

Serial Execution

To run a serial instance, simply type visit on the command
line. You can use visit -h to see what command options are
available.

Parallel Execution

Complex processing on large amounts of data can be done on multiple
processors in parallel, but requires some preparation. The first thing
you will have to do is set up a host profile on each cluster you
plan to use.

Host Profile

To create or modify a host profile, run: visit -gui

From the Options menu, select Host profiles. . .

On the Selected profile tab, make sure "Host name
aliases" are defined, based on the cluster's host name. For a
host name of the form

hostname.domain.edu

Enter the following in the "Host name aliases" box:

hostname###.domain.edu hostname###

This is an example of what it should look like:

Then, on the Parallel options tab, set the MPI startup command,
the number of nodes to use, and the number of cores. You'll have to be
aware of how many cores per node are available on the cluster you're
using. When done, it will look like this:

Profiles you define in this way are available for future use. You'll
need a profile to match each set of nodes/cores you plan to use. When
it comes time to process, the action of opening a file will pop up a
dialog box to have you select the proper profile. Based on the example
above, it will look like:

When the parallel version of Visit is executed, and the above
profile is used, the following text should appear: